Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle
Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle
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DOI：
10.1101/gr.170101
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发表时间：
2001-04-01
期刊：
影响因子：
7
通讯作者：
Keele, JW
中科院分区：
文献类型：
--
作者：
Smith, TPL;Grosse, WM;Keele, JW
功能基因组学研究的一个重要组成部分是在感兴趣的组织中表达的DNA序列。为了提供牛特异性表达序列数据的资源并促进牛研究中的这种强大方法，制备了四个标准化cDNA文库并进行高通量测序。用从多种组织汇集的RNA制备文库，以提高标准化效率并使获得序列数据的独立基因的数量最大化。靶组织包括最有可能影响动物健康、生长、繁殖效率和胴体品质等生产参数的组织。通过从每个文库中收集6000- 23，000个序列（GenBank中保存的总共68，520个序列）来评估标准化的成功以及序列间和序列内冗余。将这些序列与GenBank dbEST数据库中存在的56，500个其他牛EST序列组合进行序列比较和组装，以构建牛基因索引（可从基因组研究所获得，网址为http：//www.tigr.org/tdb/tgi.shtml）。在分析时存在于GenBank中的124，381个牛EST形成了16，740个组件，这些组件在网站上列出并注释。单个文库序列数据的分析表明，合并组织方法在制备用于高效深度测序的文库方面非常有效。
An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this powerful approach in cattle research, four normalized cDNA libraries were produced and arrayed for high-throughput sequencing. The libraries were made with RNA pooled from multiple tissues to increase efficiency of normalization and maximize the number of independent genes for which sequence data were obtained. Target tissues included those with highest likelihood to have impact on production parameters of animal health, growth, reproductive efficiency, and carcass merit. Success of normalization and inter- and intralibrary redundancy were assessed by collecting 6000-23,000 sequences from each of the libraries (68,520 total sequences deposited in GenBank). Sequence comparison and assembly of these sequences was performed in combination with 56,500 other bovine EST sequences present in the GenBank dbEST database to construct a cattle Gene Index (available from The Institute For Genomic Research at http://www.tigr.org/tdb/tgi.shtml). The 124,381 bovine ESTs present in GenBank at the time of the analysis form 16,740 assemblies that are listed and annotated on the Web site. Analysis of individual library sequence data indicates that the pooled-tissue approach was highly effective in preparing libraries for efficient deep sequencing.